If Ferrari feel RBR is advantaged by also managing STR, there's nothing preventing them fielding a second team, calling it "Scuderia Dino" and letting LDM be the boss of them both. In fact, they keep clamouring for a third car, that would give them two third cars.
I don't think it's that monumentous an advantage (unless they're sharing team orders during a race). For one thing, there's only so much Adrian Newey to go around. For another, to a lesser degree, there are several other people who "command" certain aspects of the operations of several teams. All the engine builders do this, as do Pirelli. Which did become a bone of contention at one point last season when Pirelli decided RBR were running too much camber.